PMID- 26714466
OWN - NLM
STAT- MEDLINE
DCOM- 20160928
LR  - 20181113
IS  - 1471-2164 (Electronic)
IS  - 1471-2164 (Linking)
VI  - 16
DP  - 2015 Dec 29
TI  - Selection processes in simple sequence repeats suggest a correlation with their 
      genomic location: insights from a fungal model system.
PG  - 1107
LID - 10.1186/s12864-015-2274-x [doi]
LID - 1107
AB  - BACKGROUND: Adaptive processes shape the evolution of genomes and the diverse 
      functions of different genomic regions are likely to have an impact on the 
      trajectory and outcome of this evolution. The main underlying hypothesis of this 
      study is that the evolution of Simple Sequence Repeats (SSRs) is correlated with 
      the evolution of the genomic region in which they are located, resulting in 
      differences of motif size, number of repeats, and levels of polymorphisms. These 
      differences should be clearly detectable when analyzing the frequency and type of 
      SSRs within the genome of a species, when studying populations within a species, 
      and when comparing closely related sister taxa. By coupling a genome-wide SSR 
      survey in the genome of the plant pathogenic fungus Heterobasidion irregulare 
      with an analysis of intra- and interspecific variability of 39 SSR markers in 
      five populations of the two sibling species H. irregulare and H. annosum, we 
      investigated mechanisms of evolution of SSRs. RESULTS: Results showed a clear 
      dominance of trirepeats and a selection against other repeat number, i.e. di- and 
      tetranucleotides, both in regions inside Open Reading Frames (ORFs) and upstream 
      5' untranslated region (5'UTR). Locus per locus AMOVA showed SSRs both inside 
      ORFs and upstream 5'UTR were more conserved within species compared to SSRs in 
      other genomic regions, suggesting their evolution is constrained by the functions 
      of the regions they are in. Principal coordinates analysis (PCoA) indicated that 
      even if SSRs inside ORFs were less polymorphic than those in intergenic regions, 
      they were more powerful in differentiating species. These findings indicate SSRs 
      evolution undergoes a directional selection pressure comparable to that of the 
      ORFs they interrupt and to that of regions involved in regulatory functions. 
      CONCLUSIONS: Our work linked the variation and the type of SSRs with regions 
      upstream 5'UTR, putatively harbouring regulatory elements, and shows that the 
      evolution of SSRs might be affected by their location in the genome. 
      Additionally, this study provides a first glimpse on a possible molecular basis 
      for fast adaptation to the environment mediated by SSRs.
FAU - Gonthier, Paolo
AU  - Gonthier P
AD  - Department of Agricultural, Forest and Food Sciences, University of Torino, 
      10095, Grugliasco, Italy. paolo.gonthier@unito.it.
FAU - Sillo, Fabiano
AU  - Sillo F
AD  - Department of Agricultural, Forest and Food Sciences, University of Torino, 
      10095, Grugliasco, Italy. fabiano.sillo@unito.it.
FAU - Lagostina, Elisa
AU  - Lagostina E
AD  - Department of Environmental Sciences, Policy and Management, University of 
      California at Berkeley, CA, 94720, Berkeley, USA. elisa.lagostina@gmail.com.
AD  - Department of Earth and Environmental Sciences, University of Pavia, 27100, 
      Pavia, Italy. elisa.lagostina@gmail.com.
FAU - Roccotelli, Angela
AU  - Roccotelli A
AD  - Department of Environmental Sciences, Policy and Management, University of 
      California at Berkeley, CA, 94720, Berkeley, USA. aroccotelli@yahoo.it.
AD  - Department of Agriculture, Mediterranean University of Reggio Calabria, 89122, 
      Reggio Calabria, Italy. aroccotelli@yahoo.it.
FAU - Cacciola, Olga Santa
AU  - Cacciola OS
AD  - Department of Agriculture, Food and Environment, University of Catania, 95123, 
      Catania, Italy. olgacacciola@unict.it.
FAU - Stenlid, Jan
AU  - Stenlid J
AD  - Department of Forest Mycology and Plant Pathology, Swedish University of 
      Agricultural Sciences, 75007, Uppsala, Sweden. Jan.Stenlid@slu.se.
FAU - Garbelotto, Matteo
AU  - Garbelotto M
AD  - Department of Environmental Sciences, Policy and Management, University of 
      California at Berkeley, CA, 94720, Berkeley, USA. matteog@berkeley.edu.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20151229
PL  - England
TA  - BMC Genomics
JT  - BMC genomics
JID - 100965258
RN  - 0 (5' Untranslated Regions)
SB  - IM
MH  - 5' Untranslated Regions/genetics
MH  - Genome, Plant/*genetics
MH  - Genomics
MH  - Microsatellite Repeats/genetics
MH  - Open Reading Frames/genetics
MH  - Polymorphism, Genetic/genetics
PMC - PMC4696308
EDAT- 2015/12/31 06:00
MHDA- 2016/09/30 06:00
PMCR- 2015/12/29
CRDT- 2015/12/31 06:00
PHST- 2015/09/10 00:00 [received]
PHST- 2015/12/03 00:00 [accepted]
PHST- 2015/12/31 06:00 [entrez]
PHST- 2015/12/31 06:00 [pubmed]
PHST- 2016/09/30 06:00 [medline]
PHST- 2015/12/29 00:00 [pmc-release]
AID - 10.1186/s12864-015-2274-x [pii]
AID - 2274 [pii]
AID - 10.1186/s12864-015-2274-x [doi]
PST - epublish
SO  - BMC Genomics. 2015 Dec 29;16:1107. doi: 10.1186/s12864-015-2274-x.